ChemDoodle will help guide your drawing to create the most aesthetic figures using a feature we call the "Optimize Zone" for standard bond angles and lengths. Just move your mouse out of the zone to override it.

In addition to the standard elemental labels, you can input any custom label you desire. ChemDoodle will automatically chemically interpret and format labels. You can also directly control text formatting. Labels can be expanded to full atom models and full atom models can be automatically collapsed into concise labels based on your abbreviation library or to a custom label.

Abbreviations and compound labels like "COOH" and "Ph", as well as formulae can be expanded to quickly build and work with complex chemical structures. You can define your own custom abbreviations to be used in ChemDoodle.

In addition to the predefined Jmol, Rasmol, PyMOL and CDK color sets, you can also manually define your own elemntal color set to apply to molecule rendering.

If you need to tag atoms or bonds by increments, ChemDoodle provides powerful tools to do this. Simply click on the atom or bond to tag them and the next tag is automatically incremented. Tag by alphabet, number, roman numeral or greek letter.

ChemDoodle will automatically place your charges, radicals, stereocenter labels and other attributes for you in an aesthetic manner. You can override these decisions at any time by holding down and dragging the mouse during placement.

Several methods are available to control the z-ordering of bonds, or how they layer on top of each other when overlaps occur. Easy to use context-menu options are provided for quick control. ChemDoodle also includes an advanced algorithm to automatically layer bonds for you based on the assigned wedges within a drawn structure.

In addition to standard ring tools and templates, ChemDoodle provides special arbitrary ring and crown ether tools for quickly building advanced ring systems.

Quickly build structures using our built-in template libraries, or create your own templates. The Templates widget organizes the templates for you.

Several tools are provided to help you quickly build complex 3D geometries, including carbon nanotube and prism builders. Armchair, zigzag and chiral nanotubes can be built. Use the Rotate in 3D tool to change the 3D perspective of the drawn structure.

Complex algorithms have been implemented to automatically lay out chemical structures aesthetically. Select only part of a structure to clean only that part, leaving the remaining structure untouched.

Search databases (PubChem, ChemSpider, ChemExper) for chemical structures and drag them right into your document using the MolGrabber widget.

There are so many tools in ChemDoodle for working with chemical graphics, including alignment and distribution functions, bond adjustment features, action tracking, transforms and more.

Automatically detect bonds in chemical files that do not contain bond data. Commonly, molecule data files do not include any bond information. Files including PDB, XYZ and output from quantum mechanics programs do not officially store bond data. Instead of having to draw bonds by hand, ChemDoodle contains tools for deducing covalent bonds based on just the atom elements and coordinates alone. ChemDoodle can even assign bond orders to those bonds based on several algorithms, including "All Single", Antechamber and Auto-UFF.

Calculate and depict ring systems in your structures, including the Smallest Set of Smallest Rings (SSSR), the Euler Facet Ring Set, and the Hanser Ring Set.

Detect the aromaticity and anti-aromaticity of your rings and display the number of pi electron contributors. You can also force aromatic ring recognition using all resonance bonds. Tools are available to switch your figures between Kekulé, delocalized and circle forms.

Automatically produce a Kekulé structure will alternating single and double bonds from a single bond skeleton or any resonance system. This is useful when dealing with large, embedded, aromatic ring systems.

Repeat units (aka repeat groups or repeating brackets) are used to define linearly repeating substructures in molecules. A repeat unit consists of a pair of square brackets denoting the substructure to be repeated and a repeat value defining how many times the substructure is repeated. Most conveniently, when properly defined in chemical structures in ChemDoodle, repeat units are automatically recognized, evaluated and expanded so you can quickly draw complex structures and perform cheminformatics tasks such as calculating molecular masses and formulas. This is very convenient for oligomers and polymers.

Generate 3D coordinates for your drawn structures using a template method or Universal Force Field (UFF) optimization.

Calculate dozens of descriptors for structures, including masses, formulae, volumes, physical properties, topological indexes, counts, bioactivity filters and more.

Use the Elemental Analysis widget to calculate molecular masses, elemental analysis and isotopic distributions for structures as you draw them. Isotopes, radicals and charges are supported. Select entire complexes to calculate bulk properties.

ChemDoodle will double check your work for you and notify you when it finds chemistry issues, such as overvalanced atoms, incorrectly drawn stereocenters, or partially intersecting repeat units.

ChemDoodle contains an entire elemental database. Most of the calculations performed by ChemDoodle use this data. The data is kept relevant and referenced and includes many elemental properties such as electronegativites, radii, thermodynamic properties, years of discovery and more. Databases of ionization energies and isotopes are also provided. You may view this data at any time in the View menu.

A fully interactive periodic table is provided for visualization and reference. You can even customize it and print it out!

Initiate CAS SciFinderⁿ queries and gain access to a history of chemical information right from ChemDoodle. Draw your query in ChemDoodle and search SciFinderⁿ by Substances, Suppliers, Reactions or References. A SciFinderⁿ account is required.

Google Patents searching is integrated. You may perform structure, substructure and similarity searching into the Google Patents and non-patent literature databases at Google using structures drawn in ChemDoodle.

All of the resources we use to develop the algorithms in ChemDoodle or the choices we make for the software are documented in the Help menu. This way you can evaluate the quality of our work.

The IUPAC specification is a very thorough and complex ruleset for properly conveying 3D geometric features in a 2D chemical drawing. ChemDoodle uses the IUPAC specification for interpretation of geometric features by default, and will always modify or output 2D figures to satisfy IUPAC rules, if possible, when using the features of the software.

As an alternative to the IUPAC rules, the MDL/BIOVIA specification is implemented as an option in ChemDoodle for more relaxed and less stringent interpretation of 3D geometries in 2D chemical drawings.

Stereochemical projections will be automatically recognized and stereochemical features will be analyzed. Fischer, Haworth and chair projections are supported.

If you have or need files that contain stereochemical information, ChemDoodle is the perfect tool for you. ChemDoodle automatically handles stereochemical information in and out of popular chemical file formats, like MDL CTfiles, SMILES, ChemDraw, InChI and more.

The CIP rules have long been the standard for describing configurations of stereochemical features in a molecule. While flawed, they have seen many revisions over the decades and were clarified by the work of Paulina Mata. These rules were adopted by IUPAC for naming standards and fully described in the Blue books. The most recent CIP rules from IUPAC were then algorithmically analyzed and standarized by Hanson et al. to remove any ambiguities and describe a completely consistent system for CIP assignments.

ChemDoodle implements all 6 current CIP rules as well as auxilliary desciptors and mancude ring support. Stereochemical features in your structures will be assigned "R", "S", "E", "Z", "M" and "P" descriptors. The CIP algorithm in ChemDoodle is validated against the test suite provided by Hanson et. al. and is 100% accurate in all 300 test cases provided.

Pseudo-asymmetric stereochemical features in your structure are also resolved by our CIP engine, including meso centers. These will be assigned the lowercase "r", "s", "e", "z", "m" and "p" descriptors.

The less systematic "cis" and "trans" stereochemistry descriptors can also be assigned for double bonds in unambiguous cases.

ChemDoodle will assign all of the stereochemical configurations in your drawn structures with a single menu click.

If you do not want to draw the stereochemistry in your structures, ChemDoodle will do it for you, if necessary and possible. Just tell it which configuration to apply for a given stereochemical feature.

ChemDoodle will check your stereochemical drawings for you to make sure they are compliant with the IUPAC and MDL/BIOVIA specifications. ChemDoodle will also let you know when stereochemical information is not ideal, such as when wedges are drawn on a center that is not a stereocenter, or if a potential stereocenter does not have a configuration specified.

When you draw a stereochemical configuration for a chiral center in ChemDoodle, it is recognized by the software exactly as drawn, being one of two enantiomers. In certain cases, you may wish to define a current chiral center as one configuration or the other (or), or as a mixture of both (and). This can be defined using the enhanced stereochemistry features in ChemDoodle. You may then output this information into several file formats for use by compatible registration and search engines.

ChemDoodle 2D provides unique tools to automatically render single electron, electron pair and bond forming pushing arrows based on an starting and ending atom or bond. Quickly create advanced mechanism drawings.

Arrows and arrowheads are completely customizable, just like everything else in ChemDoodle 2D. Change sizes, fills, colors and more. You may also change the arrow stroke to create a wavy photon arrow, or include a no go slash or cross.

You can manually define reactants and products, or have ChemDoodle 2D automatically infer reaction components based on their locations around an arrow.

ChemDoodle 2D contains convenient tools for building reactions based on bond breaking and formation. Simply drag the tool over the desired bonds and the appropriate reactions will automatically be generated for you.

Reactions can be automatically laid out for you, to achieve the most aesthetic figures. Reactions that are very wide will be stacked appropriately.

Quickly define atom-to-atom mappings for your reactions, and ChemDoodle will help check your work. Input and output of reaction atom-to-atom mapping is fully supported in ChemDoodle Documents, ChemDoodle JSON, ChemDraw CDX and CDXML, SMILES, and MDL RXN files.

Complete reactions can be balanced by ChemDoodle 2D, either when drawn using structures and arrows, or typed as a reaction equation. ChemDoodle 2D will be able to balance any reaction equation that can be balanced. For infinitely irreducible solutions, a proprietary algorithm that minimizes positive integers for coefficients will be determined to balance your equation.

ChemDoodle 2D provides an industry leading stoichiometry table. This stoichiometry table is a form where you input theoretical and experimental values from your experiment and you will get accurate calculations for your input and results. ChemDoodle 2D's stoichiometry tables are fully chemically aware and are self-calculating. Input drawn reactions or typed chemical equations are automatically balanced (however you can override these stoichiometric ratios with the Equivalents row) and the limiting component is automatically inferred based on the input values. ChemDoodle 2D enforces the credibility of the calculations for the entire table, and will even warn you if your input is suspicious, for instance, if you have a percent yield greater than 100%.

Read and write many popular chemical file types for working with the applications you use:

ACD/ChemSketch Documents (.sk2), ChemDoodle Documents (.icl), ChemDoodle 3D Scenes (.ic3), ChemDoodle Javascript Data (.cwc.js), CambridgeSoft ChemDraw Exchange (.cdx), CambridgeSoft ChemDraw XML (.cdxml), Crystallographic Information Format (.cif), CHARMM CARD File (.crd), ChemAxon Marvin Document (.mrv), Chemical Markup Language (.cml), Daylight SMILES (.smi, .smiles), Gaussian Cube (.cub, .cube), Gaussian Input (.gjf, .gau, .gzmat, .com), IUPAC InChI (.inchi), IUPAC JCAMP-DX (.jdx, .dx), ISIS Sketch File (.skc), ISIS Sketch Transportable Graphics File (.tgf), MDL MOLFiles, both V2000 and V3000 connection tables (.mol, .mdl), MDL SDFiles (.sdf, .sd), MDL RDFiles (.rdf, .rd), MDL RXNFiles, both V2000 and V3000 connection tables (.rxn), MMI SketchEl Molecule (.el), Molinspiration JME String (.jme), RCSB BinaryCIF (.bcif), RCSB Macromolecular Crystallographic Information File (.cif, .mcif, .mmcif), RCSB Protein Data Bank Files (.pdb, .ent), RCSB Protein Data Bank Markup Language (.xml, .pdbml), Schrödinger MacroModel (.mmd, .mmod), Schrödinger Maestro (.mae), Standard Molecular Data (.smd), Tripos Mol2 (.mol2, .ml2, .sy2), Tripos Sybyl Line Notation (.sln), Beilstein ROSDAL (.ros), XYZ Files (.xyz)

Quickly analyze chemical line notations from websites and generate them for searches using the Line Notation Pad widget.

Write a large number of bitmap (also known as raster or pixel) images for use with other applications. Some formats have additional options, such as controlling output resolution in PNG, JPEG, and TIFF images.

1. CompuServ Graphics Interchange Format {.gif}
2. Joint Photographic Experts Group {.jpg, .jpeg, .jpe, .jfif, .jfi, .jif}
3. Microsoft Bitmap {.bmp, .dib}
4. Portable Network Graphics {.png}
5. Tagged Image File Format {.tiff, .tif}
6. UNIX Portable PixMap {.ppm, pnm, pbm, pgm}
7. Wireless Bitmap {.wbmp}

Write a large number of vector graphics formats for use with other graphics applications when scalability is required. Most of the vector formats allow for text to shape conversion (compatibility) or preserving text output (for future editing, such as in LaTeX document creation). Most of the vector formats also allow embedding of chemical data to be recovered later.

1. Adobe Portable Document Format {.pdf}
2. Encapsulated Postscript {.eps, .epi, .epsi, .epsf}
3. Macintosh Vector Pict {.pict}
4. OpenDocument Graphics {.odg}
5. Web Scalable Vector Graphics {.svg, .svgz}
6. Windows Enhanced Metafile {.emf}

By default, ChemDoodle will automatically size output images to fit content, but you may override this behavior to any custom image size while instructing ChemDoodle to scale or buffer your drawings. A convenient preview is provided when saving images to visualize output size and how your drawing will fit.

Produce 2D ChemDoodle Web Components, which are high-quality, interactive, HTML5 components for websites and web apps that work in Microsoft Edge, Mozilla Firefox, Google Chrome, Apple Safari and Opera, and even on Mobile Safari on iOS and Chrome for Android.

Full support for high resolution displays, such as Retina Macs and the Microsoft Surface Pro.

Switch between interface "Light" and "Dark" mode themes to reduce strain on your eyes.

Control interface colors, interface font sizes, define cursors and a cursor left-handed and right-handed mode make it comfortable for most users to use the software. You can also fully define all of the menu item accelerators (except the ones forced by the operating system) and tool shortcuts.

Paste scalable vector graphics into your favorite word processors, including Microsoft Office, Apple iWork and OpenOffice.

Round-trip editing allows you to insert content into 3rd party applications, and then place that same content back into ChemDoodle from that 3rd party application for further editing. Round-trip editing is supported on Windows through OLE, macOS via PDF and on Linux with OpenOffice.

NOTE: It takes two applications to work together for round trip editing. While ChemDoodle provides functionality for round trip editing, the other application you want to round trip with may not support round trip editing. Other applications that do support round trip editing may remove round trip editing functionality at any time and without the consent of iChemLabs.

A Quicklook plugin for macOS allows you to preview all of the chemical formats ChemDoodle understands conveniently in Finder. Not on Mac? No worries, ChemDoodle’s file chooser contains previews on all operating systems.

Search your computer and attached storage devices for chemical structures using the Search widget.

Produce interactive HTML5 components that work in Microsoft Edge, Mozilla Firefox, Google Chrome, Apple Safari and Opera, and even on Mobile Safari on iOS and Chrome for Android.

A ChemDoodle license includes access to our ChemDoodle Mobile app companion for iOS (iPod/iPhone/iPad), Android and other mobile devices.

ChemDoodle works with several partners to help you improve your workflow. These partners include databases like PubChem, GSRS, ChemExper and ChemSpider as well as ELNs such as LabArchives.

We are always adding new features, and our customers continuously enjoy new updates with great new innovative solutions and tools that they have requested. Your license entitles you to all updates.

A thorough user manual is free to download. It is in PDF format, fully searchable with a fully linked table of contents and index.